Context: Limb lengthening correction according to Ilizarov distraction osteogenesis (DO) usually yields excellent results. While pediatric orthopedic surgeons anecdotally report that botulinum toxin A (Botox) alleviates spasm and pain during DO, no study has examined the effects of this surgery and Botox injection on muscle morphology in children. Aims: (1) To evaluate the clinical and radiological effects of lower limb lengthening in children and (2) the effects of adjunctive Botox muscle injection. Setting and Design: This was a center and randomized control trial. Methods: Seven children underwent tibial (n = 3) or femoral lengthening (n = 4) and were randomized to receive either a Botox or sterile saline solution. Quality of life and functional mobility outcomes, muscle testing, and magnetic resonance imaging examination were obtained at baseline, 12-, and 24-month postoperative. Muscle measurements were acquired on axial T1-weighted images and included: (1) total cross-sectional area (TCSA), (2) functional cross-sectional area (FCSA, fat-free area), (3) ratio of FCSA to TCSA, and (4) asymmetry between sides. Results: Physical performance improved at 12- and 24-month postoperative. Muscle strength remained functional across the three time points. A decrease in TCSA and FCSA was observed at 12-month follow-up in the operated thigh of patients undergoing femur lengthening, but muscle mass was regained at 24 months. However, TCSA and FCSA remained lower in the operated femur at 24 months. Similar findings were also observed in patients who underwent tibial lengthening. Patients in the Botox group appeared to have a slightly greater decrease in muscle mass and increase in fatty infiltration in the operated leg. Conclusions: Children undergoing DO preserved their muscle strength and improved physical performance 2-year postoperative. Our results suggest that muscle size and muscle mass remained lower in the operated leg; a finding that was slightly more prominent in children who received a Botox injection.